Understanding how distributions of species change through time allows evaluation of hypotheses about factors shaping biogeographic patterns and evolutionary trajectories of genetic lineages. Ideally, such studies would assess whether population genetic processes are associated with geographic distribution shifts, loss or gain of distributional area through time, or fragmentation of distributional areas, information that can now be derived via ecological niche modeling. We examined the distributional changes through time in lineages and populations of Brown Creeper (Certhia americana), a widespread North American bird, to test biogeographic and population genetic hypotheses. In two populations with genetic support for population bottlenecks, Monterey County in California and the Sierra Madre Oriental in Mexico, ecological niche models indicated range contractions and increased fragmentation since the Last Glacial Maximum (LGM). Projections of niche models to the future suggested continuation of range contractions and fragmentation. Of the 3 major allopatric lineages of Brown Creeper (eastern North America, western North America, and southern North America and Central America), the most stable through time was the southern lineage, which corresponds with increased genetic diversity. The potential geographic distribution of the western lineage has remained stable in size but not location since the LGM, corresponding with a genetic signal of isolation by distance. The eastern lineage experienced range contractions during the LGM, likely resulting in the contemporary lack of genetic structure within the lineage. Finally, there is limited evidence of potential range overlap during the LGM between the western lineage and the other 2 lineages, although the overlap is limited to the Arizona sky islands between the west and south lineages. These results suggest that ecological niche modeling and population genetic data may be used as mutual predictors when investigating phylogeographic patterns and processes.